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Hengel SR, Oppenheimer KG, Smith CM, Schaich MA, Rein HL, Martino J, Darrah KE, Witham M, Ezekwenna OC, Burton KR, Van Houten B, Spies M, Bernstein KA. The human Shu complex promotes RAD51 activity by modulating RPA dynamics on ssDNA. Nat Commun 2024; 15:7197. [PMID: 39169038 PMCID: PMC11339404 DOI: 10.1038/s41467-024-51595-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/09/2024] [Indexed: 08/23/2024] Open
Abstract
Templated DNA repair that occurs during homologous recombination and replication stress relies on RAD51. RAD51 activity is positively regulated by BRCA2 and the RAD51 paralogs. The Shu complex is a RAD51 paralog-containing complex consisting of SWSAP1, SWS1, and SPIDR. We demonstrate that SWSAP1-SWS1 binds RAD51, maintains RAD51 filament stability, and enables strand exchange. Using single-molecule confocal fluorescence microscopy combined with optical tweezers, we show that SWSAP1-SWS1 decorates RAD51 filaments proficient for homologous recombination. We also find SWSAP1-SWS1 enhances RPA diffusion on ssDNA. Importantly, we show human sgSWSAP1 and sgSWS1 knockout cells are sensitive to pharmacological inhibition of PARP and APE1. Lastly, we identify cancer variants in SWSAP1 that alter Shu complex formation. Together, we show that SWSAP1-SWS1 stimulates RAD51-dependent high-fidelity repair and may be an important new cancer therapeutic target.
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Affiliation(s)
- Sarah R Hengel
- University of Pittsburgh, School of Medicine, Department of Pharmacology and Chemical Biology, UPMC-Hillman Cancer Center, Pittsburgh, PA, USA.
- Tufts University, Department of Biology, Medford, MA, USA.
| | - Katherine G Oppenheimer
- University of Pittsburgh, School of Medicine, Department of Pharmacology and Chemical Biology, UPMC-Hillman Cancer Center, Pittsburgh, PA, USA
| | - Chelsea M Smith
- University of Pittsburgh, School of Medicine, Department of Pharmacology and Chemical Biology, UPMC-Hillman Cancer Center, Pittsburgh, PA, USA
- University of North Carolina at Chapel Hill, Department of Pathology and Laboratory Medicine, Chapel Hill, NC, USA
| | - Matthew A Schaich
- University of Pittsburgh, School of Medicine, Department of Pharmacology and Chemical Biology, UPMC-Hillman Cancer Center, Pittsburgh, PA, USA
| | - Hayley L Rein
- University of Pittsburgh, School of Medicine, Department of Pharmacology and Chemical Biology, UPMC-Hillman Cancer Center, Pittsburgh, PA, USA
| | - Julieta Martino
- University of Pittsburgh, School of Medicine, Department of Pharmacology and Chemical Biology, UPMC-Hillman Cancer Center, Pittsburgh, PA, USA
- GeneDx, Gaithersburg, MD, USA
| | - Kristie E Darrah
- University of Pennsylvania School of Medicine, Penn Center for Genome Integrity, Department of Biochemistry and Biophysics, 421 Curie Boulevard, Philadelphia, PA, USA
| | - Maggie Witham
- Tufts University, Department of Biology, Medford, MA, USA
| | | | - Kyle R Burton
- Tufts University, Department of Biology, Medford, MA, USA
| | - Bennett Van Houten
- University of Pittsburgh, School of Medicine, Department of Pharmacology and Chemical Biology, UPMC-Hillman Cancer Center, Pittsburgh, PA, USA
| | - Maria Spies
- University of Iowa, Department of Biochemistry and Molecular Biology, Iowa City, IA, USA
| | - Kara A Bernstein
- University of Pittsburgh, School of Medicine, Department of Pharmacology and Chemical Biology, UPMC-Hillman Cancer Center, Pittsburgh, PA, USA.
- University of Pennsylvania School of Medicine, Penn Center for Genome Integrity, Department of Biochemistry and Biophysics, 421 Curie Boulevard, Philadelphia, PA, USA.
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2
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Hengel SR, Oppenheimer K, Smith C, Schaich MA, Rein HL, Martino J, Darrah K, Ezekwenna O, Burton K, Van Houten B, Spies M, Bernstein KA. The human Shu complex promotes RAD51 activity by modulating RPA dynamics on ssDNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.14.580393. [PMID: 38405734 PMCID: PMC10888808 DOI: 10.1101/2024.02.14.580393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Templated DNA repair that occurs during homologous recombination and replication stress relies on RAD51. RAD51 activity is positively regulated by BRCA2 and the RAD51 paralogs. The Shu complex is a RAD51 paralog-containing complex consisting of SWSAP1 and SWS1. We demonstrate that SWSAP1-SWS1 binds RAD51, maintains RAD51 filament stability, and enables strand exchange. Using single molecule confocal fluorescence microscopy combined with optical tweezers, we show that SWSAP1-SWS1 decorates RAD51 filaments proficient for homologous recombination. We also find SWSAP1-SWS1 enhances RPA diffusion on ssDNA. Importantly, we show human sgSWSAP1 and sgSWS1 knockout cells are sensitive to pharmacological inhibition of PARP and APE1. Lastly, we identify cancer variants in SWSAP1 that alter SWS1 complex formation. Together, we show that SWSAP1-SWS1 stimulates RAD51-dependent high-fidelity repair and may be an important new cancer therapeutic target.
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3
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Kolenko P, Svoboda J, Černý J, Charnavets T, Schneider B. Structural variability of CG-rich DNA 18-mers accommodating double T-T mismatches. Acta Crystallogr D Struct Biol 2020; 76:1233-1243. [PMID: 33263329 PMCID: PMC7709200 DOI: 10.1107/s2059798320014151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/23/2020] [Indexed: 11/26/2022] Open
Abstract
Solution and crystal data are reported for DNA 18-mers with sequences related to those of bacterial noncoding single-stranded DNA segments called repetitive extragenic palindromes (REPs). Solution CD and melting data showed that the CG-rich, near-palindromic REPs from various bacterial species exhibit dynamic temperature-dependent and concentration-dependent equilibria, including architectures compatible with not only hairpins, which are expected to be biologically relevant, but also antiparallel duplexes and bimolecular tetraplexes. Three 18-mer oligonucleotides named Hpar-18 (PDB entry 6rou), Chom-18 (PDB entry 6ros) and its brominated variant Chom-18Br (PDB entry 6ror) crystallized as isomorphic right-handed A-like duplexes. The low-resolution crystal structures were solved with the help of experimental phases for Chom-18Br. The center of the duplexes is formed by two successive T-T noncanonical base pairs (mismatches). They do not deform the double-helical geometry. The presence of T-T mismatches prompted an analysis of the geometries of these and other noncanonical pairs in other DNA crystals in terms of their fit to the experimental electron densities (RSCC) and their geometric fit to the NtC (dinucleotide conformational) classes (https://dnatco.datmos.org/). Throughout this work, knowledge of the NtC classes was used to refine and validate the crystal structures, and to analyze the mismatches.
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Affiliation(s)
- Petr Kolenko
- Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague, Brehova 7, 11519 Prague 1, Czech Republic
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Jakub Svoboda
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Jiří Černý
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Tatsiana Charnavets
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Bohdan Schneider
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
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4
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Shibata T, Iwasaki W, Hirota K. The intrinsic ability of double-stranded DNA to carry out D-loop and R-loop formation. Comput Struct Biotechnol J 2020; 18:3350-3360. [PMID: 33294131 PMCID: PMC7677664 DOI: 10.1016/j.csbj.2020.10.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 10/22/2020] [Accepted: 10/25/2020] [Indexed: 12/03/2022] Open
Abstract
Double-stranded (ds)DNA, not dsRNA, has an ability to form a homologous complex with single-stranded (ss)DNA or ssRNA of homologous sequence. D-loops and homologous triplexes are homologous complexes formed with ssDNA by RecA/Rad51-family homologous-pairing proteins, and are a key intermediate of homologous (genetic/DNA) recombination. R-loop formation independent of transcription (R-loop formation in trans) was recently found to play roles in gene regulation and development of mammals and plants. In addition, the crRNA-Cas effector complex in CRISPR-Cas systems also relies on R-loop formation to recognize specific target. In homologous complex formation, ssDNA/ssRNA finds a homologous sequence in dsDNA by Watson-Crick base-pairing. crRNA-Cas effector complexes appear to actively melt dsDNA to make its bases available for annealing to crRNA. On the other hand, in D-loop formation and homologous-triplex formation, it is likely that dsDNA recognizes the homologous sequence before the melting of its double helix by using its intrinsic molecular function depending on CH2 at the 2'-position of the deoxyribose, and that the major role of RecA is the extension of ssDNA and the holding dsDNA at a position suitable for homology search. This intrinsic dsDNA function would also play a role in R-loop formation. The dependency of homologous-complex formation on 2'-CH2 of the deoxyribose would explain the absence of homologous complex formation by dsRNA, and dsDNA as sole genome molecule in all cellular organisms.
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Affiliation(s)
- Takehiko Shibata
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
| | - Wakana Iwasaki
- Laboratory for Translation Structural Biology, RIKEN Center for Biosystems Dynamics Research, Tsurumi, Yokohama, Japan
| | - Kouji Hirota
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
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5
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Mladenov E, Li F, Zhang L, Klammer H, Iliakis G. Intercellular communication of DNA damage and oxidative status underpin bystander effects. Int J Radiat Biol 2018; 94:719-726. [PMID: 29377786 DOI: 10.1080/09553002.2018.1434323] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
PURPOSE A well-known phenomenon in the field of radiation biology is that cells exposed to ionizing radiation (IR) (targeted cells) can induce in non-irradiated (non-targeted), bystander cells effects reminiscent of DNA damage responses (DDR) normally expected, exclusively in targeted cells. These phenomena are collectively referred to as radiation-induced bystander effects (RIBE) and have different manifestations depending on the endpoint studied. Although it is now recognized that RIBE reflects to a considerable extent communication by the targeted cells to undamaged cells of their damaged status, the molecular underpinnings of this communication and its significance for the organism are only partly understood. In particular, it remains unknown why and how targeted cells induce DNA damage in non-targeted, bystander cells threatening their genomic stability and risking thus their transformation to cancer cells. Here, we outline observations hinting to possible sources of artifacts in experiments designed to detect RIBE and summarize a model according to which targeted cells modulate their redox status as part of their overall response to IR and use this modified redox status as a source to generate signals that are transmitted to non-irradiated cells of the organism. MATERIAL AND METHODS A synthesis of published evidence is presented. RESULTS Depending on type, RIBE signals may be transmitted through various forms of direct intercellular contact, through molecules acting locally in a paracrine fashion, or through molecules acting remotely in an endocrine fashion. We reason that DNA damage generated in bystander cells is unlikely to manifest the clustered character exhibited in directly exposed cells and postulate that RIBE will depend on complications generated when simpler forms of damage encounter the DNA replication fork. CONCLUSIONS We suggest that RIBE result from intercellular communication mechanisms designed to spread within tissues, or the organism, alarm signals of DNA damage inflicted in subsets of the constituent cells. This response likely evolved to protect organisms by appropriately modulating stress response, repair or apoptosis, and may in some instances also cause adverse effects, e.g. as collateral damage.
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Affiliation(s)
- Emil Mladenov
- a Institute of Medical Radiation Biology , University of Duisburg-Essen Medical School , Essen , Germany
| | - Fanghua Li
- a Institute of Medical Radiation Biology , University of Duisburg-Essen Medical School , Essen , Germany
| | - Lihua Zhang
- a Institute of Medical Radiation Biology , University of Duisburg-Essen Medical School , Essen , Germany
| | - Holger Klammer
- a Institute of Medical Radiation Biology , University of Duisburg-Essen Medical School , Essen , Germany
| | - George Iliakis
- a Institute of Medical Radiation Biology , University of Duisburg-Essen Medical School , Essen , Germany
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6
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Wang Y, An R, Umanah GK, Park H, Nambiar K, Eacker SM, Kim B, Bao L, Harraz MM, Chang C, Chen R, Wang JE, Kam TI, Jeong JS, Xie Z, Neifert S, Qian J, Andrabi SA, Blackshaw S, Zhu H, Song H, Ming GL, Dawson VL, Dawson TM. A nuclease that mediates cell death induced by DNA damage and poly(ADP-ribose) polymerase-1. Science 2017; 354:354/6308/aad6872. [PMID: 27846469 PMCID: PMC5134926 DOI: 10.1126/science.aad6872] [Citation(s) in RCA: 247] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 08/22/2016] [Indexed: 12/26/2022]
Abstract
Inhibition or genetic deletion of poly(ADP-ribose) (PAR) polymerase-1 (PARP-1) is protective against toxic insults in many organ systems. The molecular mechanisms underlying PARP-1-dependent cell death involve release of mitochondrial apoptosis-inducing factor (AIF) and its translocation to the nucleus, which results in chromatinolysis. We identified macrophage migration inhibitory factor (MIF) as a PARP-1-dependent AIF-associated nuclease (PAAN). AIF was required for recruitment of MIF to the nucleus, where MIF cleaves genomic DNA into large fragments. Depletion of MIF, disruption of the AIF-MIF interaction, or mutation of glutamic acid at position 22 in the catalytic nuclease domain blocked MIF nuclease activity and inhibited chromatinolysis, cell death induced by glutamate excitotoxicity, and focal stroke. Inhibition of MIF's nuclease activity is a potential therapeutic target for diseases caused by excessive PARP-1 activation.
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Affiliation(s)
- Yingfei Wang
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA. .,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ran An
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Neurology of Huashan Hospital, State Key Laboratory of Medical Neurobiology, Fudan University, Shanghai 200032, China
| | - George K Umanah
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hyejin Park
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA 70130-2685, USA
| | - Kalyani Nambiar
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Stephen M Eacker
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA 70130-2685, USA
| | - BongWoo Kim
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lei Bao
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Maged M Harraz
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Calvin Chang
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Rong Chen
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jennifer E Wang
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Tae-In Kam
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA 70130-2685, USA
| | - Jun Seop Jeong
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Center for High-Throughput Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Zhi Xie
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Stewart Neifert
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA 70130-2685, USA
| | - Jiang Qian
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Shaida A Andrabi
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Seth Blackshaw
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Center for High-Throughput Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Heng Zhu
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Center for High-Throughput Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hongjun Song
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Guo-Li Ming
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Valina L Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA. .,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA 70130-2685, USA.,Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ted M Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA. .,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA 70130-2685, USA.,Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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7
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Konomura N, Arai N, Shinohara T, Kobayashi J, Iwasaki W, Ikawa S, Kusano K, Shibata T. Rad51 and RecA juxtapose dsDNA ends ready for DNA ligase-catalyzed end-joining under recombinase-suppressive conditions. Nucleic Acids Res 2017; 45:337-352. [PMID: 27794044 PMCID: PMC5224515 DOI: 10.1093/nar/gkw998] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 10/06/2016] [Accepted: 10/18/2016] [Indexed: 12/20/2022] Open
Abstract
RecA-family recombinase-catalyzed ATP-dependent homologous joint formation is critical for homologous recombination, in which RecA or Rad51 binds first to single-stranded (ss)DNA and then interacts with double-stranded (ds)DNA. However, when RecA or Rad51 interacts with dsDNA before binding to ssDNA, the homologous joint-forming activity of RecA or Rad51 is quickly suppressed. We found that under these and adenosine diphosphate (ADP)-generating suppressive conditions for the recombinase activity, RecA or Rad51 at similar optimal concentrations enhances the DNA ligase-catalyzed dsDNA end-joining (DNA ligation) about 30- to 40-fold. The DNA ligation enhancement by RecA or Rad51 transforms most of the substrate DNA into multimers within 2-5 min, and for this enhancement, ADP is the common and best cofactor. Adenosine triphosphate (ATP) is effective for RecA, but not for Rad51. Rad51/RecA-enhanced DNA ligation depends on dsDNA-binding, as shown by a mutant, and is independent of physical interactions with the DNA ligase. These observations demonstrate the common and unique activities of RecA and Rad51 to juxtapose dsDNA-ends in preparation for covalent joining by a DNA ligase. This new in vitro function of Rad51 provides a simple explanation for our genetic observation that Rad51 plays a role in the fidelity of the end-joining of a reporter plasmid DNA, by yeast canonical non-homologous end-joining (NHEJ) in vivo.
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Affiliation(s)
- Naoto Konomura
- Cellular & Molecular Biology Laboratory, RIKEN, Wako-shi, Saitama 351-0198, Japan
- Advanced Catalysis Research Group, RIKEN Center for Sustainable Resource Science, Wako-shi, Saitama 351-0198, Japan
- Department of Supramolecular Biology, Graduate School of Nanobiosciences, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Naoto Arai
- Department of Applied Biological Science, Nihon University College of Bioresource Sciences, Fujisawa-shi, Kanagawa 252-0880, Japan
| | - Takeshi Shinohara
- Cellular & Molecular Biology Laboratory, RIKEN, Wako-shi, Saitama 351-0198, Japan
- Advanced Catalysis Research Group, RIKEN Center for Sustainable Resource Science, Wako-shi, Saitama 351-0198, Japan
- Department of Supramolecular Biology, Graduate School of Nanobiosciences, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Jun Kobayashi
- Department of Applied Biological Science, Nihon University College of Bioresource Sciences, Fujisawa-shi, Kanagawa 252-0880, Japan
| | - Wakana Iwasaki
- Cellular & Molecular Biology Laboratory, RIKEN, Wako-shi, Saitama 351-0198, Japan
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Shukuko Ikawa
- Cellular & Molecular Biology Laboratory, RIKEN, Wako-shi, Saitama 351-0198, Japan
- Advanced Catalysis Research Group, RIKEN Center for Sustainable Resource Science, Wako-shi, Saitama 351-0198, Japan
| | - Kohji Kusano
- Center for Genetic Resource Education & Development, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Takehiko Shibata
- Cellular & Molecular Biology Laboratory, RIKEN, Wako-shi, Saitama 351-0198, Japan
- Advanced Catalysis Research Group, RIKEN Center for Sustainable Resource Science, Wako-shi, Saitama 351-0198, Japan
- Department of Supramolecular Biology, Graduate School of Nanobiosciences, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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8
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Volodin AA, Bocharova TN, Smirnova EA. Polycationic ligands of different chemical classes stimulate DNA strand displacement between short oligonucleotides in a protein-free system. Biopolymers 2016; 105:633-41. [DOI: 10.1002/bip.22859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 03/26/2016] [Accepted: 04/19/2016] [Indexed: 11/07/2022]
Affiliation(s)
- Alexander A. Volodin
- Institute of Molecular Genetics of the Russian Academy of Sciences; Kurchatov Sq, 2 Moscow 123182 Russia
| | - Tatiana N. Bocharova
- Institute of Molecular Genetics of the Russian Academy of Sciences; Kurchatov Sq, 2 Moscow 123182 Russia
| | - Elena A. Smirnova
- Institute of Molecular Genetics of the Russian Academy of Sciences; Kurchatov Sq, 2 Moscow 123182 Russia
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9
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Shinohara T, Ikawa S, Iwasaki W, Hiraki T, Hikima T, Mikawa T, Arai N, Kamiya N, Shibata T. Loop L1 governs the DNA-binding specificity and order for RecA-catalyzed reactions in homologous recombination and DNA repair. Nucleic Acids Res 2015; 43:973-86. [PMID: 25561575 PMCID: PMC4333409 DOI: 10.1093/nar/gku1364] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 12/14/2014] [Accepted: 12/18/2014] [Indexed: 11/16/2022] Open
Abstract
In all organisms, RecA-family recombinases catalyze homologous joint formation in homologous genetic recombination, which is essential for genome stability and diversification. In homologous joint formation, ATP-bound RecA/Rad51-recombinases first bind single-stranded DNA at its primary site and then interact with double-stranded DNA at another site. The underlying reason and the regulatory mechanism for this conserved binding order remain unknown. A comparison of the loop L1 structures in a DNA-free RecA crystal that we originally determined and in the reported DNA-bound active RecA crystals suggested that the aspartate at position 161 in loop L1 in DNA-free RecA prevented double-stranded, but not single-stranded, DNA-binding to the primary site. This was confirmed by the effects of the Ala-replacement of Asp-161 (D161A), analyzed directly by gel-mobility shift assays and indirectly by DNA-dependent ATPase activity and SOS repressor cleavage. When RecA/Rad51-recombinases interact with double-stranded DNA before single-stranded DNA, homologous joint-formation is suppressed, likely by forming a dead-end product. We found that the D161A-replacement reduced this suppression, probably by allowing double-stranded DNA to bind preferentially and reversibly to the primary site. Thus, Asp-161 in the flexible loop L1 of wild-type RecA determines the preference for single-stranded DNA-binding to the primary site and regulates the DNA-binding order in RecA-catalyzed recombinase reactions.
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Affiliation(s)
- Takeshi Shinohara
- Cellular & Molecular Biology Unit, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan Advanced Catalysis Research Group, RIKEN Center for Sustainable Resource Science, Wako-shi, Saitama 351-0198, Japan Department of Supramolecular Biology, Graduate School of Nanobiosciences, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Shukuko Ikawa
- Cellular & Molecular Biology Unit, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan Advanced Catalysis Research Group, RIKEN Center for Sustainable Resource Science, Wako-shi, Saitama 351-0198, Japan
| | - Wakana Iwasaki
- Cellular & Molecular Biology Unit, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Toshiki Hiraki
- Advanced Photon Technology Division, Research Infrastructure Group, RIKEN SPring-8 Center, RIKEN Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Takaaki Hikima
- Advanced Photon Technology Division, Research Infrastructure Group, RIKEN SPring-8 Center, RIKEN Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Tsutomu Mikawa
- Cellular & Molecular Biology Unit, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Naoto Arai
- Department of Applied Biological Science, Nihon University College of Bioresource Sciences, 1866 Kameino, Fujisawa-shi, Kanagawa 252-8510, Japan
| | - Nobuo Kamiya
- Advanced Photon Technology Division, Research Infrastructure Group, RIKEN SPring-8 Center, RIKEN Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Takehiko Shibata
- Cellular & Molecular Biology Unit, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan Advanced Catalysis Research Group, RIKEN Center for Sustainable Resource Science, Wako-shi, Saitama 351-0198, Japan Department of Supramolecular Biology, Graduate School of Nanobiosciences, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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10
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Klammer H, Mladenov E, Li F, Iliakis G. Bystander effects as manifestation of intercellular communication of DNA damage and of the cellular oxidative status. Cancer Lett 2013; 356:58-71. [PMID: 24370566 DOI: 10.1016/j.canlet.2013.12.017] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 12/13/2013] [Accepted: 12/14/2013] [Indexed: 12/30/2022]
Abstract
It is becoming increasingly clear that cells exposed to ionizing radiation (IR) and other genotoxic agents (targeted cells) can communicate their DNA damage response (DDR) status to cells that have not been directly irradiated (bystander cells). The term radiation-induced bystander effects (RIBE) describes facets of this phenomenon, but its molecular underpinnings are incompletely characterized. Consequences of DDR in bystander cells have been extensively studied and include transformation and mutation induction; micronuclei, chromosome aberration and sister chromatid exchange formation; as well as modulations in gene expression, proliferation and differentiation patterns. A fundamental question arising from such observations is why targeted cells induce DNA damage in non-targeted, bystander cells threatening thus their genomic stability and risking the induction of cancer. Here, we review and synthesize available literature to gather support for a model according to which targeted cells modulate as part of DDR their redox status and use it as a source to generate signals for neighboring cells. Such signals can be either small molecules transported to adjacent non-targeted cells via gap-junction intercellular communication (GJIC), or secreted factors that can reach remote, non-targeted cells by diffusion or through the circulation. We review evidence that such signals can induce in the recipient cell modulations of redox status similar to those seen in the originating targeted cell - occasionally though self-amplifying feedback loops. The resulting increase of oxidative stress in bystander cells induces, often in conjunction with DNA replication, the observed DDR-like responses that are at times strong enough to cause apoptosis. We reason that RIBE reflect the function of intercellular communication mechanisms designed to spread within tissues, or the entire organism, information about DNA damage inflicted to individual, constituent cells. Such responses are thought to protect the organism by enhancing repair in a community of cells and by eliminating severely damaged cells.
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Affiliation(s)
- Holger Klammer
- Institute of Medical Radiation Biology, University of Duisburg-Essen Medical School, Essen, Germany
| | - Emil Mladenov
- Institute of Medical Radiation Biology, University of Duisburg-Essen Medical School, Essen, Germany
| | - Fanghua Li
- Institute of Medical Radiation Biology, University of Duisburg-Essen Medical School, Essen, Germany
| | - George Iliakis
- Institute of Medical Radiation Biology, University of Duisburg-Essen Medical School, Essen, Germany.
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11
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Yadav T, Carrasco B, Hejna J, Suzuki Y, Takeyasu K, Alonso JC. Bacillus subtilis DprA recruits RecA onto single-stranded DNA and mediates annealing of complementary strands coated by SsbB and SsbA. J Biol Chem 2013; 288:22437-50. [PMID: 23779106 DOI: 10.1074/jbc.m113.478347] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Naturally transformable bacteria recombine internalized ssDNA with a homologous resident duplex (chromosomal transformation) or complementary internalized ssDNAs (plasmid or viral transformation). Bacillus subtilis competence-induced DprA, RecA, SsbB, and SsbA proteins are involved in the early processing of the internalized ssDNA, with DprA physically interacting with RecA. SsbB and SsbA bind and melt secondary structures in ssDNA but limit RecA loading onto ssDNA. DprA binds to ssDNA and facilitates partial dislodging of both single-stranded binding (SSB) proteins from ssDNA. In the absence of homologous duplex DNA, DprA does not significantly increase RecA nucleation onto protein-free ssDNA. DprA facilitates RecA nucleation and filament extension onto SsbB-coated or SsbB plus SsbA-coated ssDNA. DprA facilitates RecA-mediated DNA strand exchange in the presence of both SSB proteins. DprA, which plays a crucial role in plasmid transformation, anneals complementary strands preferentially coated by SsbB to form duplex circular plasmid molecules. Our results provide a mechanistic framework for conceptualizing the coordinated events modulated by SsbB in concert with SsbA and DprA that are crucial for RecA-dependent chromosomal transformation and RecA-independent plasmid transformation.
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Affiliation(s)
- Tribhuwan Yadav
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
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12
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Ling F, Hori A, Yoshitani A, Niu R, Yoshida M, Shibata T. Din7 and Mhr1 expression levels regulate double-strand-break-induced replication and recombination of mtDNA at ori5 in yeast. Nucleic Acids Res 2013; 41:5799-816. [PMID: 23598996 PMCID: PMC3675488 DOI: 10.1093/nar/gkt273] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The Ntg1 and Mhr1 proteins initiate rolling-circle mitochondrial (mt) DNA replication to achieve homoplasmy, and they also induce homologous recombination to maintain mitochondrial genome integrity. Although replication and recombination profoundly influence mitochondrial inheritance, the regulatory mechanisms that determine the choice between these pathways remain unknown. In Saccharomyces cerevisiae, double-strand breaks (DSBs) introduced by Ntg1 at the mitochondrial replication origin ori5 induce homologous DNA pairing by Mhr1, and reactive oxygen species (ROS) enhance production of DSBs. Here, we show that a mitochondrial nuclease encoded by the nuclear gene DIN7 (DNA damage inducible gene) has 5′-exodeoxyribonuclease activity. Using a small ρ− mtDNA bearing ori5 (hypersuppressive; HS) as a model mtDNA, we revealed that DIN7 is required for ROS-enhanced mtDNA replication and recombination that are both induced at ori5. Din7 overproduction enhanced Mhr1-dependent mtDNA replication and increased the number of residual DSBs at ori5 in HS-ρ− cells and increased deletion mutagenesis at the ori5 region in ρ+ cells. However, simultaneous overproduction of Mhr1 suppressed all of these phenotypes and enhanced homologous recombination. Our results suggest that after homologous pairing, the relative activity levels of Din7 and Mhr1 modulate the preference for replication versus homologous recombination to repair DSBs at ori5.
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Affiliation(s)
- Feng Ling
- Chemical Genetics Laboratory, RIKEN, Hirosawa 2-1, Wako-shi, Saitama 351-0198, Japan.
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13
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Fornander LH, Frykholm K, Reymer A, Renodon-Cornière A, Takahashi M, Nordén B. Ca2+ improves organization of single-stranded DNA bases in human Rad51 filament, explaining stimulatory effect on gene recombination. Nucleic Acids Res 2012; 40:4904-13. [PMID: 22362735 PMCID: PMC3367181 DOI: 10.1093/nar/gks140] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Human RAD51 protein (HsRad51) catalyses the DNA strand exchange reaction for homologous recombination. To clarify the molecular mechanism of the reaction in vitro being more effective in the presence of Ca2+ than of Mg2+, we have investigated the effect of these ions on the structure of HsRad51 filament complexes with single- and double-stranded DNA, the reaction intermediates. Flow linear dichroism spectroscopy shows that the two ionic conditions induce significantly different structures in the HsRad51/single-stranded DNA complex, while the HsRad51/double-stranded DNA complex does not demonstrate this ionic dependence. In the HsRad51/single-stranded DNA filament, the primary intermediate of the strand exchange reaction, ATP/Ca2+ induces an ordered conformation of DNA, with preferentially perpendicular orientation of nucleobases relative to the filament axis, while the presence of ATP/Mg2+, ADP/Mg2+ or ADP/Ca2+ does not. A high strand exchange activity is observed for the filament formed with ATP/Ca2+, whereas the other filaments exhibit lower activity. Molecular modelling suggests that the structural variation is caused by the divalent cation interfering with the L2 loop close to the DNA-binding site. It is proposed that the larger Ca2+ stabilizes the loop conformation and thereby the protein–DNA interaction. A tight binding of DNA, with bases perpendicularly oriented, could facilitate strand exchange.
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Affiliation(s)
- Louise H Fornander
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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14
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Ling F, Mikawa T, Shibata T. Enlightenment of yeast mitochondrial homoplasmy: diversified roles of gene conversion. Genes (Basel) 2011; 2:169-90. [PMID: 24710143 PMCID: PMC3924846 DOI: 10.3390/genes2010169] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2011] [Revised: 01/18/2011] [Accepted: 01/25/2011] [Indexed: 11/29/2022] Open
Abstract
Mitochondria have their own genomic DNA. Unlike the nuclear genome, each cell contains hundreds to thousands of copies of mitochondrial DNA (mtDNA). The copies of mtDNA tend to have heterogeneous sequences, due to the high frequency of mutagenesis, but are quickly homogenized within a cell ("homoplasmy") during vegetative cell growth or through a few sexual generations. Heteroplasmy is strongly associated with mitochondrial diseases, diabetes and aging. Recent studies revealed that the yeast cell has the machinery to homogenize mtDNA, using a common DNA processing pathway with gene conversion; i.e., both genetic events are initiated by a double-stranded break, which is processed into 3' single-stranded tails. One of the tails is base-paired with the complementary sequence of the recipient double-stranded DNA to form a D-loop (homologous pairing), in which repair DNA synthesis is initiated to restore the sequence lost by the breakage. Gene conversion generates sequence diversity, depending on the divergence between the donor and recipient sequences, especially when it occurs among a number of copies of a DNA sequence family with some sequence variations, such as in immunoglobulin diversification in chicken. MtDNA can be regarded as a sequence family, in which the members tend to be diversified by a high frequency of spontaneous mutagenesis. Thus, it would be interesting to determine why and how double-stranded breakage and D-loop formation induce sequence homogenization in mitochondria and sequence diversification in nuclear DNA. We will review the mechanisms and roles of mtDNA homoplasmy, in contrast to nuclear gene conversion, which diversifies gene and genome sequences, to provide clues toward understanding how the common DNA processing pathway results in such divergent outcomes.
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Affiliation(s)
- Feng Ling
- Chemical Genetics Laboratory, RIKEN Advanced Science Institute/2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan.
| | - Tsutomu Mikawa
- Biometal Science Laboratory, RIKEN SPring-8 Center/Mikazuki cho, Hyogo 679-5148 Japan.
| | - Takehiko Shibata
- Division of Molecular and Cellular Physiology, Department of Supramolecular Biology, Graduate School of Nanobiosciences, Yokohama City University/1-7-29 Suehiro cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
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15
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Manfredi C, Suzuki Y, Yadav T, Takeyasu K, Alonso JC. RecO-mediated DNA homology search and annealing is facilitated by SsbA. Nucleic Acids Res 2010; 38:6920-9. [PMID: 20581116 PMCID: PMC2978338 DOI: 10.1093/nar/gkq533] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Bacillus subtilis RecO plays a central role in recombinational repair and genetic recombination by (i) stimulating RecA filamentation onto SsbA-coated single-stranded (ss) DNA, (ii) modulating the extent of RecA-mediated DNA strand exchange and (iii) promoting annealing of complementary DNA strands. Here, we report that RecO-mediated strand annealing is facilitated by cognate SsbA, but not by a heterologous one. Analysis of non-productive intermediates reveals that RecO interacts with SsbA-coated ssDNA, resulting in transient ternary complexes. The self-interaction of ternary complexes via RecO led to the formation of large nucleoprotein complexes. In the presence of homology, SsbA, at the nucleoprotein, removes DNA secondary structures, inhibits spontaneous strand annealing and facilitates RecO loading onto SsbA–ssDNA complex. RecO relieves SsbA inhibition of strand annealing and facilitates transient and random interactions between homologous naked ssDNA molecules. Finally, both proteins lose affinity for duplex DNA. Our results provide a mechanistic framework for rationalizing protein release and dsDNA zippering as coordinated events that are crucial for RecA-independent plasmid transformation.
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Affiliation(s)
- Candela Manfredi
- Centro Nacional de Biotecnología, CSIC, C/Darwin 3, 28049 Madrid, Spain
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16
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Egli M, Pallan PS. The many twists and turns of DNA: template, telomere, tool, and target. Curr Opin Struct Biol 2010; 20:262-75. [PMID: 20381338 DOI: 10.1016/j.sbi.2010.03.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2010] [Accepted: 03/15/2010] [Indexed: 11/16/2022]
Abstract
If any proof were needed of DNA's versatile roles and use, it is certainly provided by the numerous depositions of new three-dimensional (3D) structures to the coordinate databanks (PDB, NDB) over the last two years. Quadruplex motifs involving G-repeats, adducted sequences and oligo-2'-deoxynucleotides (ODNs) with bound ligands are particularly well represented. In addition, structures of chemically modified DNAs (CNAs) and artificial analogs are yielding insight into stability, pairing properties, and dynamics, including those of the native nucleic acids. Besides being of significance for establishing diagnostic tools and in the analysis of protein-DNA interactions, chemical modification in conjunction with investigations of the structural consequences may yield novel nucleic acid-based therapeutics. DNA's predictable and highly specific pairing behavior makes it the material of choice for constructing 3D-nanostructures of defined architecture. Recently the first examples of DNA nanoparticle and self-assembled 3D-crystals were reported. Although the structures discussed in this review are all based either on X-ray crystallography or solution NMR, small angle X-ray scattering (SAXS), and cryoEM are proving to be useful approaches for the characterization of nanoscale DNA architecture.
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Affiliation(s)
- Martin Egli
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232-0146, USA.
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17
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Chen LT, Wang AHJ. A rationally designed peptide enhances homologous recombination in vitro and resistance to DNA damaging agents in vivo. Nucleic Acids Res 2010; 38:4361-71. [PMID: 20308162 PMCID: PMC2910059 DOI: 10.1093/nar/gkq182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The RecA family of proteins is essential in homologous recombination, a critical step in DNA repair. Here, we report that a rationally-designed small peptide based on the crystal structure of Escherichia coli RecA–DNA complex can promote homologous recombination through the enhancement of both RecA-mediated strand assimilation and three-strand exchange activity. Among 17 peptides tested, peptide #3 with the amino acid sequence of IRFLTARRR has the most potent activity in promoting the RecA-mediated D-loop formation by ∼7.2-fold at 37°C. Other peptides such as IRFLTAKKK and IRLLTARRR also have similar, albeit lower, activities. Therefore, hydrophobicity and poly-positive charges, and the space between them in those small peptides are crucial features for such activities. The enhancement of recombination by these peptides appears to be a general phenomenon as similar results were seen by using different plasmids. Remarkably, peptide #3 alone without RecA can also promote the D-loop formation at elevated temperature. Cell viability assays showed that the peptide elevates mammalian cell resistance to two cytotoxic DNA drugs, cisplatin and doxorubicin. The rescue of viability may result from increased DNA repair efficiency. Such peptides may find future biological applications.
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Affiliation(s)
- Li-Tzu Chen
- Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan
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18
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Masuda T, Ling F, Shibata T, Mikawa T. Analysis of DNA-binding sites on Mhr1, a yeast mitochondrial ATP-independent homologous pairing protein. FEBS J 2010; 277:1440-52. [PMID: 20148947 DOI: 10.1111/j.1742-4658.2010.07574.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Mhr1 protein is necessary for mtDNA homologous recombination in Saccharomyces cerevisiae. Homologous pairing (HP) is an essential reaction during homologous recombination, and is generally catalyzed by the RecA/Rad51 family of proteins in an ATP-dependent manner. Mhr1 catalyzes HP through a mechanism similar, at the DNA level, to that of the RecA/Rad51 proteins, but without utilizing ATP. However, it has no sequence homology with the RecA/Rad51 family proteins or with other ATP-independent HP proteins, and exhibits different requirements for DNA topology. We are interested in the structural features of the functional domains of Mhr1. In this study, we employed the native fluorescence of Mhr1's Trp residues to examine the energy transfer from the Trp residues to etheno-modified ssDNA bound to Mhr1. Our results showed that two of the seven Trp residues (Trp71 and Trp165) are spatially close to the bound DNA. A systematic analysis of mutant Mhr1 proteins revealed that Asp69 is involved in Mg(2+)-dependent DNA binding, and that multiple Lys and Arg residues located around Trp71 and Trp165 are involved in the DNA-binding activity of Mhr1. In addition, in vivo complementation analyses showed that a region around Trp165 is important for the maintenance of mtDNA. On the basis of these results, we discuss the function of the region surrounding Trp165.
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Affiliation(s)
- Tokiha Masuda
- Graduate School of Nanobioscience, Yokohama City University, Japan
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